Similar regions between promoters of rpsD

<<<<<< sub TACCATGTTTTTATCACCTAAAAGTTTACCACTAATTTTTGTTTATTATATCATAAACGG hal ................................................TATCGAAAAACC -300 -290 -280 -270 -260 -250 sub TGAAGCAATAATGGAGGAATGGTTGACTTCAAAACAAA-TAAATTATATAATGACCTTTG hal TTAAGTAGCCAGGGATATCTCCTTGACTTCAATTGTTTGTGGAGGTTATAATGGACTCTG -240 -230 -220 -210 -200 -190 sub TGTGAAATATTGCAGCCTTTTTGTTC--AGCTTCTATGTTTT----CATTTTGTTCCTTA hal TGTGAAATAAGACAGCCAAGGTGAACTTAACATGTACACCCTTCGGCATTTTGTTCCTCA -180 -170 -160 -150 -140 -130 sub ----------TCAA-------TAAGGTGTATCGTGTAACTCTCT-GCTGCTGGAGCGAGG hal AACCAGCGGCTGAACTTGTTTTGAGGTGTACCACGTAAC-CTCTAGCTGTCGAGGCGAAG -120 -110 -100 -90 sub ATACATGAAAACAAAATGTGCATGGTCGAATAGAGC-AGACGGTTTTTATTTTCCA-CAA hal GTACAGAACAACAAAATGAGCATGTTAAAGGATTGCCAAACTGTTGTTATTTTGCATCAT -80 -70 -60 -50 -40 -30 sub AAATAAAACCAAAGGAGGAGTCACATT hal TCAAAATAACAAAGGAGGAGTC..... -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...